Another thing I had thought of was waking up for Daily Life at some point, and engaging in the usual events with a slightly different internal monologue and ways in which characters interact with you. And then you discover that the character you had been playing up until that point has been killed.
I love this idea, there's so much potential in it. The shock of seeing the player character dead would be fantastic if it was done well enough.
Though I think for Danganronpa 4 it's best if we stick to a female character for the entirety of the game haha.
Also as definitive as that ending feels I still think a 4th game is definitely coming. A new writer perhaps but I'm always ready for more Danganronpa.